Here are my thoughts on the subject:
The C-Dory 22 was designed with the Johnson 70 2-stroke and a Johnson 9.9 kicker on the stern in mind (and in reality). No amount of hammering the keyboard will change that; it is what it is. The boat will always be "at its best" if that weight is adhered to.
However...a lot of things have changed over the years. There is more fuel in the stern (50 gallons versus 36), usually more batteries, and generally heavier engines and the CD22 does alright. Is it as "good" as the original configuration? Depends on how you use it and what you're after. Is the suspension on a Porsche 911 better than on my Suburban? Not if you're towing a C-Dory but sure as heck if we're slicing and dicing on a mountain road.
It's all about balance; when a designer gets things right the ends of the boat react as they should for the best handling and ride (at the designed speed). If you radically change the weight at one end the boat is no longer "in balance"; at least not as the designer planned it. For instance, you drive your pickup around with no weight in the bed and that's what you're used to. Now you pick up about 1000 pounds of gravel and I can guarantee you're going to notice a difference in the ride and handling. Good? Bad? Not important (as long as you don't exceed safety limits) but it is DIFFERENT.
There's a world of difference in how the CD22 handles in tough conditions with a single E-TEC 75/90 on it versus say the old Honda BF90 and BF9.9 kicker. It's not even like driving the same boat if you're running Deception Pass on a nasty day in the same conditions. But...some folks may never need concern themselves with that because they never operate the boat that way. I could hand my mother the keys to the most superbly tuned sports car in existence and after a day of use she'd never be able to tell me if it handled better than her current daily driver; she'd never drive to the point where "better" ever started to show up.
Keeping the weight down on the transom of the C-Dory 22 yields the best handling and performance from a technical standpoint and I encourage folks that will routinely operate in rough conditions to kick that a little higher on the priority list. If average to calm conditions are more the norm than the heavier weight on the transom is not as much of a factor. And generally we're not talking about safety here since the boats with heavier main engines and kickers do fine. We're specifically talking about refining your choices to get what you want (and anticipate) out of the boat.
There was a major revision in the hull in 1986; the earlier boat were truly flat-bottomed and then they became as we know them now. The hull has not been redesigned for heavier four stroke engines but I'd argue that since the consumer has control over the engine choices that's not a huge issue.
You have to be careful on the twins and really watch the weight as you can go from lightweight Honda BF40 or BF50 (at 205 pounds apiece) to some really heavy ones (around 260 pound apiece). Again, it's all about what you're looking for in terms of handling, performance, use, and cost.